RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9114
(98 letters)
>1wih_A Mitochondrial ribosome recycling factor; structural genomics,
riken structural genomics/proteomics initiative, RSGI,
unknown function; NMR {Mus musculus} SCOP: d.67.3.1
Length = 84
Score = 65.0 bits (159), Expect = 9e-16
Identities = 29/72 (40%), Positives = 47/72 (65%)
Query: 27 PGAIESLKVEFEDDEYVLQDLAQISRKNPKTLIINMSSFPQLIPVTMKALVDSGMNMNPQ 86
++ + V D + L + QIS K+P+ +++NM+SFP+ +KA+ +SGMN+NP+
Sbjct: 5 SSGLDHITVVTADGKVALNQIGQISMKSPQVILVNMASFPECTAAAIKAIRESGMNLNPE 64
Query: 87 QEGTTIIIPIPK 98
EGT I +PIPK
Sbjct: 65 VEGTLIRVPIPK 76
>1eh1_A Ribosome recycling factor; translation, hinge variability; 2.60A
{Thermus thermophilus} SCOP: d.67.3.1 PDB: 2qbe_6 2qbg_6
2qbi_6* 2qbk_6* 2v46_Y* 2v48_Y* 2z4l_6* 2z4n_6* 3j0d_J
3j0e_G
Length = 185
Score = 35.2 bits (82), Expect = 0.001
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 7/74 (9%)
Query: 27 PGAIESLKVEFEDDEYVLQDLAQISRKNPKTLIINMSSFP---QLIPVTMKALVDSGMNM 83
P + LKVE+ L +A ++ +P+TL++ + KA+ DS + +
Sbjct: 35 PALLLHLKVEYYGAHVPLNQIATVTAPDPRTLVVQ----SWDQNALKAIEKAIRDSDLGL 90
Query: 84 NPQQEGTTIIIPIP 97
NP +G + I IP
Sbjct: 91 NPSNKGDALYINIP 104
>1is1_A Ribosome recycling factor; translation; 2.20A {Vibrio
parahaemolyticus} SCOP: d.67.3.1 PDB: 3r8n_Y
Length = 185
Score = 34.8 bits (81), Expect = 0.001
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 7/74 (9%)
Query: 27 PGAIESLKVEFEDDEYVLQDLAQISRKNPKTLIINMSSFP---QLIPVTMKALVDSGMNM 83
P + + VE+ L +A + ++ +TL I +L KA++ S + +
Sbjct: 34 PSLLSGISVEYYGAATPLNQVANVVAEDARTLAIT----VFDKELTQKVEKAIMMSDLGL 89
Query: 84 NPQQEGTTIIIPIP 97
NP GT I +P+P
Sbjct: 90 NPMSAGTIIRVPLP 103
>4gfq_A Ribosome-recycling factor; structural genomics, niaid, national
institute of allergy AN infectious diseases; 2.65A
{Bacillus anthracis}
Length = 209
Score = 34.9 bits (81), Expect = 0.001
Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 7/57 (12%)
Query: 44 LQDLAQISRKNPKTLIINMSSFP---QLIPVTMKALVDSGMNMNPQQEGTTIIIPIP 97
+ LA I+ + L+I P I KA++ + + +NP +GT I I P
Sbjct: 75 VVQLANITVPEARLLVIQ----PYDKTSIGDIEKAILKADLGLNPSNDGTVIRIAFP 127
>1dd5_A Ribosome recycling factor; three-helix bundle, beta-alpha-beta
sandwich; 2.55A {Thermotoga maritima} SCOP: d.67.3.1
PDB: 1t1m_C
Length = 185
Score = 34.5 bits (80), Expect = 0.002
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 7/74 (9%)
Query: 27 PGAIESLKVEFEDDEYVLQDLAQISRKNPKTLIINMSSFP---QLIPVTMKALVDSGMNM 83
P +E +KV++ + LA IS +TL+I P ++ + KA+ S + +
Sbjct: 34 PAILEEIKVDYYGVPTPVNQLATISISEERTLVIK----PWDKSVLSLIEKAINASDLGL 89
Query: 84 NPQQEGTTIIIPIP 97
NP +G I + P
Sbjct: 90 NPINDGNVIRLVFP 103
>1ise_A Ribosome recycling factor; translation; 2.20A {Escherichia coli}
SCOP: d.67.3.1 PDB: 1ek8_A* 1zn0_A 1zn1_A 2rdo_8
Length = 185
Score = 34.4 bits (80), Expect = 0.002
Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 7/74 (9%)
Query: 27 PGAIESLKVEFEDDEYVLQDLAQISRKNPKTLIINMSSFP---QLIPVTMKALVDSGMNM 83
P ++ + VE+ L+ LA ++ ++ +TL IN + P KA++ S + +
Sbjct: 34 PSLLDGIVVEYYGTPTPLRQLASVTVEDSRTLKIN----VFDRSMSPAVEKAIMASDLGL 89
Query: 84 NPQQEGTTIIIPIP 97
NP G+ I +P+P
Sbjct: 90 NPNSAGSDIRVPLP 103
>1wqg_A Ribosome recycling factor; translation factor, triple-helix bundle,
protein synthesis, translation; 2.15A {Mycobacterium
tuberculosis} SCOP: d.67.3.1 PDB: 1wqf_A 1wqh_A
Length = 185
Score = 33.7 bits (78), Expect = 0.003
Identities = 12/57 (21%), Positives = 25/57 (43%), Gaps = 7/57 (12%)
Query: 44 LQDLAQISRKNPKTLIINMSSFP---QLIPVTMKALVDSGMNMNPQQEGTTIIIPIP 97
+ LA I+ + ++I P + A+ +S + +NP +G I + +P
Sbjct: 51 ITQLASINVPEARLVVIK----PYEANQLRAIETAIRNSDLGVNPTNDGALIRVAVP 103
>1wf3_A GTP-binding protein; GTPase, riken structural genomics/prote
initiative, RSGI, structural genomics, hydrolase; HET:
GNP; 1.88A {Thermus thermophilus} SCOP: c.37.1.8
d.52.3.1
Length = 301
Score = 29.7 bits (68), Expect = 0.11
Identities = 8/39 (20%), Positives = 15/39 (38%), Gaps = 4/39 (10%)
Query: 23 LFCIPGAIESLKVEFEDDEYVLQDLAQISRKNPKTLIIN 61
++ + +DE V + L + K P L+ N
Sbjct: 91 VWVVDLRHPPTP----EDELVARALKPLVGKVPILLVGN 125
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 29.2 bits (65), Expect = 0.18
Identities = 6/25 (24%), Positives = 7/25 (28%), Gaps = 4/25 (16%)
Query: 40 DEYVLQDL----AQISRKNPKTLII 60
D + I NP L I
Sbjct: 1650 DNHFKDTYGFSILDIVINNPVNLTI 1674
Score = 26.6 bits (58), Expect = 1.6
Identities = 19/85 (22%), Positives = 26/85 (30%), Gaps = 23/85 (27%)
Query: 4 QITPQPQRHSPQPILV------NTPLFCIPGAIESLKVEF----EDDEYV--LQDLAQIS 51
+ +P L N L AI F D+Y L+DL Q
Sbjct: 131 IMAKRPFDKKSNSALFRAVGEGNAQLV----AI------FGGQGNTDDYFEELRDLYQTY 180
Query: 52 RKNPKTLIINMSS-FPQLIPVTMKA 75
LI + +LI T+ A
Sbjct: 181 HVLVGDLIKFSAETLSELIRTTLDA 205
>1ge9_A Ribosome recycling factor; three-helix bundle; NMR {Aquifex
aeolicus} SCOP: d.67.3.1
Length = 184
Score = 28.3 bits (64), Expect = 0.31
Identities = 13/57 (22%), Positives = 24/57 (42%), Gaps = 8/57 (14%)
Query: 44 LQDLAQISRKNPKTLIINMSSFP---QLIPVTMKALVDSGMNMNPQQEGTTIIIPIP 97
++ L IS ++I +P KA+ +N+NP +G I + +P
Sbjct: 54 IKQLGTISVPEHNQIVIQ----VWDQNAVPAIEKAI-REELNLNPTVQGNVIRVTLP 105
>3gqv_A Enoyl reductase; medium-chain reductase (MDR superfamily),
rossmann fold, NAD binding, oxidoreductase; HET: NAP;
1.74A {Aspergillus terreus} PDB: 3b6z_A* 3b70_A*
Length = 371
Score = 26.6 bits (59), Expect = 1.4
Identities = 7/37 (18%), Positives = 10/37 (27%), Gaps = 4/37 (10%)
Query: 62 MSSFPQLIPVTMKALVDSGMNMNPQQEGTTIIIPIPK 98
M P + P AL + + P P
Sbjct: 1 MGDQPFIPPPQQTALTVNDHD-EVTVWNA---APCPM 33
>3djl_A Protein AIDB; alpha helix, beta-barrel, FAD, flavoprotein,
oxidoreductase; HET: FAD; 1.70A {Escherichia coli} PDB:
3u33_A*
Length = 541
Score = 26.2 bits (58), Expect = 1.8
Identities = 8/26 (30%), Positives = 12/26 (46%)
Query: 65 FPQLIPVTMKALVDSGMNMNPQQEGT 90
L+P K + GM M +Q G+
Sbjct: 166 DSHLLPGGQKRGLLIGMGMTEKQGGS 191
>2iw3_A Elongation factor 3A; acetylation, ATP-binding, protein
biosynthesis, nucleotide-binding, phosphorylation, RNA-
binding, rRNA-binding; HET: ADP; 2.4A {Saccharomyces
cerevisiae} PDB: 2iwh_A* 2ix3_A 2ix8_A
Length = 986
Score = 25.4 bits (55), Expect = 4.0
Identities = 7/36 (19%), Positives = 14/36 (38%), Gaps = 3/36 (8%)
Query: 44 LQDLAQISRKNPKTLIINMSSFPQLIPVTMKALVDS 79
L + + + P+LIPV + + D+
Sbjct: 155 LAAFSAMVDAAKDQV---ALRMPELIPVLSETMWDT 187
>2e6f_A Dihydroorotate dehydrogenase; chagas disease, pyrimidine
biosynthesis, fumarate reductase, energy metabolism,
redox homeostasis, flavoprotein; HET: FMN OXC; 1.26A
{Trypanosoma cruzi} PDB: 2e6a_A* 2e6d_A* 2e68_A* 2djl_A*
2djx_A* 3c3n_A* 2b4g_A* 3c61_A* 3mhu_A* 3mjy_A*
Length = 314
Score = 25.2 bits (56), Expect = 4.1
Identities = 12/66 (18%), Positives = 25/66 (37%), Gaps = 18/66 (27%)
Query: 5 ITPQPQRHSPQPILVNTPLFCI-------PGAIESLKVEFEDDEYVLQDLAQISRKNPKT 57
T P+ +P+P + PL I G ++ L+ + + + K
Sbjct: 47 CTSAPRDGNPEPRYMAFPLGSINSMGLPNLGF-----------DFYLKYASDLHDYSKKP 95
Query: 58 LIINMS 63
L +++S
Sbjct: 96 LFLSIS 101
>4dgh_A Sulfate permease family protein; STAS domain, anion exchange,
membrane, transport protein; HET: MSE; 1.90A {Vibrio
cholerae} PDB: 3mgl_A*
Length = 130
Score = 25.0 bits (55), Expect = 4.2
Identities = 11/67 (16%), Positives = 22/67 (32%), Gaps = 16/67 (23%)
Query: 5 ITPQPQRHSPQPILV---NTPLFCIPGAIESLKVEFEDDEYVLQDLAQISRKNPKTLIIN 61
+ + P+ + V P F F E + + I + P+ LI+
Sbjct: 9 LAQHGRSTLPRELAVYALEGPFF------------FAAAETFERVMGSIQ-ETPQILILR 55
Query: 62 MSSFPQL 68
+ P +
Sbjct: 56 LKWVPFM 62
>3a0r_A Sensor protein; four helix bundle, PAS fold, kinase,
phosphoprotein, transfe two-component regulatory system;
3.80A {Thermotoga maritima}
Length = 349
Score = 24.5 bits (54), Expect = 6.7
Identities = 8/34 (23%), Positives = 16/34 (47%)
Query: 19 VNTPLFCIPGAIESLKVEFEDDEYVLQDLAQISR 52
+ P+ I G I +K +D E + + + I+
Sbjct: 143 IRNPITIIGGFIMRMKKHLDDPETLKKYINIITN 176
>3lhp_S 4E10_D0_1ISEA_004_N (T93); epitope-scaffold, immune system; 2.70A
{Artificial gene} PDB: 1y69_8
Length = 123
Score = 24.1 bits (53), Expect = 7.2
Identities = 3/24 (12%), Positives = 7/24 (29%), Gaps = 2/24 (8%)
Query: 74 KALVDSGMNMNPQQEGTTIIIPIP 97
KA+ ++ + P
Sbjct: 22 KAVEAFKNKLDKF--KAAVRKVFP 43
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.317 0.134 0.386
Gapped
Lambda K H
0.267 0.0765 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,426,207
Number of extensions: 70587
Number of successful extensions: 256
Number of sequences better than 10.0: 1
Number of HSP's gapped: 256
Number of HSP's successfully gapped: 23
Length of query: 98
Length of database: 6,701,793
Length adjustment: 64
Effective length of query: 34
Effective length of database: 4,914,849
Effective search space: 167104866
Effective search space used: 167104866
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (23.4 bits)